LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
  using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line boxes, solvated by SRD particles

units           lj
atom_style      line
atom_modify     first big
dimension       2

read_data       data.line.srd
Reading data file ...
  orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  400 atoms
  400 lines
  read_data CPU = 0.003 seconds

# add small particles as hi density lattice

lattice         sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region          plane block INF INF INF INF -0.001 0.001
lattice         sq 10.0
Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
create_atoms    2 region plane
Created 33489 atoms
  using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
  create_atoms CPU = 0.001 seconds

group           big type 1
400 atoms in group big
group           small type 2
33489 atoms in group small
set             group small mass 0.01
Setting atom values ...
  33489 settings made for mass

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut  1.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 1.0 1.0

delete_atoms    overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.8
  ghost atom cutoff = 1.8
  binsize = 0.9, bins = 64 64 2
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:313)
Deleted 13605 atoms, new total = 20284

# SRD run

reset_timestep  0

velocity        small create 1.44 87287 loop geom

neighbor        0.8 multi
neigh_modify    delay 0 every 1 check yes
neigh_modify    exclude molecule/intra big include big

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      line/lj 2.5
pair_coeff      1 1 1.0  1.0 1.0 1.0 2.5
pair_coeff      2 2 0.0  0.0 0.0 1.0 0.0
pair_coeff      1 2 1.0  0.2 1.0 0.2 2.5

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.0001

fix             1 big rigid molecule
  100 rigid bodies with 400 atoms
fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip

fix             3 all deform 1 x scale 1.25 y scale 1.25
fix             4 all enforce2d

# diagnostics

compute         tsmall small temp/deform
compute         tbig big temp
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)

compute_modify  tbig extra/dof -350

compute         1 big erotate/asphere
compute         2 all ke
compute         3 all pe
variable        toteng equal (c_1+c_2+c_3)/atoms

thermo          1000
thermo_style    custom step c_tsmall f_2[9] c_1 etotal                 v_pebig v_ebig press
thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)

compute         10 big property/atom end1x end1y end2x end2y

#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump           2 all custom 500 dump1.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419

@Article{Gissinger24,
 author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
 title = {Type Label Framework for Bonded Force Fields in LAMMPS},
 journal = {J. Phys. Chem. B},
 year =    2024,
 volume =  128,
 number =  13,
 pages =   {3282–-3297}
}

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
  SRD/big particles = 19884 400
  big particle diameter max/min = 1.9988171 0.50330564
  SRD temperature & lamda = 1 0.02
  SRD max distance & max velocity = 0.08 40
  SRD grid counts: 230 230 1
  SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
  SRD per actual grid cell = 0.45503978
  SRD viscosity = 0.92062623
  big/SRD mass density ratio = 12.298053
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 15.906001 29.105426
  ave/max big velocity = 0 0
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
  binsize = 1.65, bins = 35 35 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 13.44 | 13.45 | 13.47 Mbytes
   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
         0   1.6084386      0              0              0              0              0              0            
      1000   1.4539924      1.2578325      0.0001679809   0.0010497614   0              0.053233399    0.69841607   
      2000   1.3516746      1.1693535      0.00031932331  0.0021450754   0              0.10877677     0.058141137  
      3000   1.3294093      1.1539986      0.00032558495  0.0022345521   0              0.11331414     0.085892255  
      4000   1.3049311      1.1174444      0.00039637116  0.0026520968   0              0.13448783     0.10574422   
      5000   1.2790124      1.1209176      0.0004519172   0.0032635257   0              0.16549339     0.59225702   
      6000   1.2631214      1.0868777      0.00052274216  0.003527049    0              0.17885666     0.26093936   
      7000   1.2520054      1.0780954      0.00051683183  0.0038111141   0              0.1932616     -0.0014733978 
      8000   1.2412037      1.0587149      0.00056620143  0.0038329297   0              0.19436786     0.31576462   
      9000   1.2242125      1.0699712      0.00065335672  0.0039948578   0              0.20257924     0.19755012   
     10000   1.2155758      1.0279682      0.00059730828  0.004142635    0              0.21007302     0.30022953   
Loop time of 1.92412 on 4 procs for 10000 steps with 20284 atoms

Performance: 44903.607 tau/day, 5197.177 timesteps/s, 105.420 Matom-step/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.026855   | 0.027529   | 0.028377   |   0.4 |  1.43
Neigh   | 0.0073723  | 0.007433   | 0.0075693  |   0.1 |  0.39
Comm    | 0.062837   | 0.065574   | 0.066747   |   0.6 |  3.41
Output  | 0.00072894 | 0.00076558 | 0.00083361 |   0.0 |  0.04
Modify  | 1.7861     | 1.7926     | 1.8        |   0.4 | 93.16
Other   |            | 0.03026    |            |       |  1.57

Nlocal:           5071 ave        5096 max        5051 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost:             44 ave          51 max          40 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs:              0 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 500
Dangerous builds = 0

#undump          1
#undump          2
unfix           3

change_box      all triclinic
Changing box ...
  triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)

fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip #tstat yes

#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump           2 all custom 500 dump2.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]

fix             3 all deform 1 xy erate 0.0002 units box remap v

run             30000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
  SRD/big particles = 19884 400
  big particle diameter max/min = 1.9988171 0.50330564
  SRD temperature & lamda = 1 0.02
  SRD max distance & max velocity = 0.08 40
  SRD grid counts: 288 288 1
  SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
  SRD per actual grid cell = 0.26976265
  SRD viscosity = 1.0312189
  big/SRD mass density ratio = 20.672578
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 12.826666 40
  ave/max big velocity = 0.53469722 1.7415554
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
  binsize = 1.65, bins = 44 44 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton/tri
      stencil: half/multi/2d/tri
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 17.6 | 17.6 | 17.61 Mbytes
   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
     10000   1.0416233      0              0.0005972922   0.0041426543   0              0.210074       0.016213064  
     11000   1.0366852      1.0236717      0.00066926382  0.004404743    0              0.22336452     0.097686059  
     12000   1.028695       1.0023004      0.00065323121  0.0043971164   0              0.22297777     0.30007875   
     13000   1.0223214      1.0296267      0.00060201395  0.0041815724   0              0.21204754     0.17307062   
     14000   1.0210601      1.0092227      0.00057020066  0.0041936718   0              0.2126611      0.13379405   
     15000   1.0169223      1.003359       0.00060818329  0.0046120335   0              0.23387622     0.39144341   
     16000   1.012222       0.99937463     0.00060471571  0.004533278    0              0.22988253     0.16026051   
     17000   1.0087993      0.98937449     0.00061843646  0.0048888197   0              0.24791205     0.095507016  
     18000   1.0030288      0.94092316     0.00054252694  0.0046740839   0              0.2370228     -0.070838649  
     19000   1.0010739      0.99759814     0.00054041829  0.0045481798   0              0.2306382      0.1944996    
     20000   1.004189       1.0157285      0.00053330893  0.0044999261   0              0.22819125     0.14452619   
     21000   0.99601133     1.003771       0.00053282188  0.0048954851   0              0.24825005     0.20196263   
     22000   0.99445408     1.0163465      0.00059954941  0.0051668276   0              0.26200983     0.21332194   
     23000   0.99663947     0.94920707     0.00057729723  0.0051052499   0              0.25888722     0.19282224   
     24000   0.99500015     1.0021742      0.00064312956  0.0053430656   0              0.27094686     0.18044164   
     25000   0.99388189     0.98446723     0.00060150964  0.0054017824   0              0.27392438     0.18844037   
     26000   0.99632932     0.94670024     0.00052479857  0.004905147    0              0.24874        0.17961314   
     27000   0.99112962     1.0247118      0.00053159824  0.004752248    0              0.2409865      0.12037737   
     28000   0.98887153     0.97734068     0.00052255365  0.0050199491   0              0.25456162     0.29110866   
     29000   0.98938025     0.99467239     0.00053095044  0.0050303107   0              0.25508706     0.59776339   
     30000   0.99081592     0.98822122     0.00056693985  0.0052452228   0              0.26598525     0.0150843    
     31000   0.99050903     1.0184912      0.00056742049  0.0056515686   0              0.28659104     0.07877756   
     32000   0.98929926     0.99257634     0.00058111732  0.005740055    0              0.29107819     0.19146041   
     33000   0.98698723     0.94872564     0.00056547335  0.0057628447   0              0.29223385     0.076755599  
     34000   0.98967998     0.98777081     0.00056045905  0.0055645603   0              0.28217885     0.095025284  
     35000   0.98777734     0.95746323     0.00050104756  0.0055630681  -4.7847642e-05  0.28210318     0.25667997   
     36000   0.98661597     0.98801246     0.00047074618  0.0054500805  -5.8956193e-05  0.27637358     0.18221607   
     37000   0.98390111     0.9837894      0.00044581144  0.0054703357  -7.4197741e-05  0.27740072     0.11959303   
     38000   0.98092646     1.0142057      0.0004945556   0.0056372628  -8.6736668e-05  0.2858656      0.017325263  
     39000   0.98125957     0.94219822     0.00059691168  0.0060914156  -9.9726556e-05  0.30889569     0.0081217281 
     40000   0.98362942     0.9649582      0.00062286697  0.0063736358  -0.00010700337  0.32320707     0.293121     
Loop time of 5.08621 on 4 procs for 30000 steps with 20284 atoms

Performance: 50961.296 tau/day, 5898.298 timesteps/s, 119.641 Matom-step/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.084321   | 0.084948   | 0.086233   |   0.3 |  1.67
Neigh   | 0.027521   | 0.029247   | 0.030632   |   0.7 |  0.58
Comm    | 0.19101    | 0.20262    | 0.2068     |   1.5 |  3.98
Output  | 0.0019581  | 0.0020369  | 0.0022544  |   0.3 |  0.04
Modify  | 4.681      | 4.6884     | 4.7051     |   0.4 | 92.18
Other   |            | 0.07891    |            |       |  1.55

Nlocal:           5071 ave        5197 max        4951 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost:             44 ave          50 max          41 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs:           5.75 ave          12 max           0 min
Histogram: 1 0 0 1 0 1 0 0 0 1

Total # of neighbors = 23
Ave neighs/atom = 0.0011338986
Neighbor list builds = 1500
Dangerous builds = 0
Total wall time: 0:00:07
